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Introduction
Fish genomics and metagenomics, fish gut microbiome, Antimicrobial resistance genes, bioremediation, fish taxonomy, aquatic biodiversity, extremophile metagenomics, aquatic pollution, microplastic, metabolomics
Current institution
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April 2018 - present
Education
May 1997 - January 2001
July 1994 - May 1996
April 1991 - August 1994
Publications
Publications (131)
The genus Channa, commonly known as Snakeheads comprises a diverse variety of species that hold great significance in the commercial sectors. Their complexity and genetic variety show how adaptable they are to different environmental settings and shed light on their evolutionary history. To delve into the genetic intricacies of the genus Channa, we...
The challenges of morphological identification of closely related species and larval stages of fishes led to increased demand for DNA-based methods to achieve precise species identification. The DNA-based technique has noteworthy applications in food authentication, detection of new species, understanding evolutionary history, and biomonitoring pro...
A rod‐shaped, motile, Gram‐stain‐positive bacterial strain RKN2 T , was isolated from gut of silver carp ( Hypophthalmichthys molitrix ) residing in Gobindsagar reservoir, Himachal Pradesh, India. Having the greatest sequence similarity to Sporosarcina koreensis F73 T (98.51%), Sporosarcina luteola Y1 T (98.4%) and Sporosarcina aquimarina SW28 T (9...
A growing environmental concern revolves around the widespread use of medicines, particularly antibiotics, which adversely impact water quality and various life forms. The unregulated production and utilization of antibiotics not only affect non-targeted organisms but also exert significant evolutionary pressures, leading to the rapid development o...
A growing environmental concern revolves around the widespread use of medicines, particularly antibiotics, which adversely
impact water quality and various life forms. The unregulated production and utilization of antibiotics not only affect non
targeted organisms but also exert significant evolutionary pressures, leading to the rapid development...
Microplastics have been ubiquitous in our environment for decades, and numerous studies have revealed their extensive dispersion, reaching far beyond the surface of the land, soil, aquatic ecosystems. They have infiltrated the food-chain, the food web, even the air we breathe, as well as the water we drink. Microplastics have been detected in the f...
Increasing recognition is being accorded to the widespread exploitation of fish populations globally, resulting in detrimental effects on aquatic biodiversity and the ecosystem. Unfortunately, fishing activities often yield unintended adverse consequences such as incidental catches of un-targeted species, habitat destructions, shifts in population...
The increasing availability of metagenome-assembled genomes and environmental metagenomes provides unprecedented access to the metabolic potential and functional differences within the habitats. The hot spring microbiome with its diverse habitats and relatively well-characterized microbial inhabitants offers an opportunity to investigate core and h...
The complex niche of fish gut is often characterized by the associated microorganisms that have implications in fish gut-health nexus. Although efforts to distinguish the microbial communities have highlighted their disparate structure along the gut length, remarkably little information is available about their distinct structural and functional pr...
The Beas River is one of the important rivers of the Indus River system located in Himachal Pradesh, India, that harbors a diverse range of freshwater fish species. The present study employed COI gene to investigate the ichthyofaunal diversity of river Beas. Through the sequencing of 203 specimens from Beas River, we identified 43 species, belongin...
Microplastics have been ubiquitous in our environment for decades, and numerous studies have revealed their
extensive dispersion, reaching far beyond the surface of the land, soil, aquatic ecosystems. They have infiltrated
the food-chain, the food web, even the air we breathe, as well as the water we drink. Microplastics have been
detected in the f...
Current scientific advances have considerably added to our understanding of the complex association between the microbiome and cancer. Host and microbiota have co-evolved into a “super-organism,” and several physiological processes and multifactorial disease conditions are influenced by host–microbiome interactions. In the past, microbial communiti...
Hexachlorocyclohexane (HCH), an organochlorine pesticide imposes several harmful impacts on the ecosystem. β- and δ-isomers of HCH are highly toxic, persistent, and recalcitrant to biodegradation, slow and incomplete degradation of β- and δ- isomers have been reported in a few strains. We have isolated a strain designated as Sphingopyxis strain MC4...
Unlabelled:
Humans are significantly impacting riverine systems worldwide, prompting us to investigate the effects of water pollution on the gut microbiome of Cyprinus carpio (common carp). Using 16S rRNA gene sequencing, we compared the gut microbiomes of common carp from two sites along river Yamuna with different pollution levels. Water polluti...
The hot spring microbiome is a complex assemblage of micro- and macro-organisms; however, the understanding and projection of enzymatic repertoire that access earth’s integral ecosystem processes remains ambivalent. Here, the Khirganga hot spring characterized with white microbial mat and ions rich in sulfate, chlorine, sodium, and magnesium ions i...
Background
Assessment of genetic diversity and population genetic structure is important for species that are economically important, threatened, and are at global conservation priority. Analysis of mitochondrial DNA is broadly used in species identification and population genetics studies due to the availability of sufficient reference data and be...
Antibiotics have been widely used to treat bacterial infections. However, their continued usage has increased the occurrence and spread of multidrug-resistant bacteria, thereby posing threats to public health. The hazards associated with the use of antibiotics necessitate the need to find possible alternatives to them. Microbes acquire resistance e...
Length-weight relationship was derived from Schistura rupecola inhabiting Song river of Garhwal, Himalaya. Sampling was done between April, 2012 and June, 2012. The result shows that the 'b' is significantly more than 3.0. The species exhibit an isometric growth pattern.
Fish are a significant component of the aquatic environment and are crucial in supporting and maintaining the entire ecological system, thereby making freshwater systems more resilient and sustainable. The structure of a fish community is influenced by biotic interactions and abiotic variables. In recent years, spanning from the last 5 to 10 years,...
A Gram-stain-positive, motile, and rod-shaped bacterium, designated as strain MB25T, was isolated from the gut of Cyprinus carpio from the highly polluted river Yamuna, India. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain MB25T belonged to the genus Sporosarcina, sharing the highest sequence similarity with S. luteola Y...
The gastrointestinal microbial community plays a crucial role in host health, immunity, protection, development and provides nutrients to the host. The rising human-induced pollution and heavy metal contamination in all aquatic systems globally has led us to explore the gut microbial diversity of two exotic invasive fish Cyprinus carpio (Linnaeus,...
Sulfur related prokaryotes residing in hot spring present good opportunity for exploring the limitless possibilities of integral ecosystem processes. Metagenomic analysis further expands the phylogenetic breadth of these extraordinary sulfur (S) metabolizing microorganisms as well as their complex metabolic networks and syntrophic interactions in e...
The hot spring microbiome is a complex assemblage of micro- and macro- organisms, however, the understanding and projection of enzymatic repertoire that access earth’s integral ecosystem processes remains limited. The composite microbial communities drive global carbon, sulfur, oxygen, iron and nitrogen cycles and other metabolic mechanism involved...
Bioremediation is an eco-friendly and highly efficient technology over other
kinds of treatments to remediate contaminated sites. However, it is necessary to take
care of every parameter related to microbial diversity and physiology and the
metabolism of the microbes during bioremediation, which helps in determining the
efficiency and the key facto...
Graphical Abstract
Sulfur Related Prokaryotes (SRP) residing in hot spring present good opportunity for exploring the limitless possibilities of integral ecosystem processes. Metagenomic analysis further expand the phylogenetic breadth of these extraordinary sulfur metabolizing microorganisms, as well a their complex metabolic networks and syntrop...
Khirganga, a pristine hot spring that lies in the Parvati Valley within the Northern Himalayas characterised with unique white colour microbial mat and divine water with healing abilities. Here, we report 41 metagenome-assembled genomes (MAGs) reconstructed from the microbial mat, sediment and water samples of hot spring passed through Genome Stand...
Hexachlorocyclohexane (HCH) is a persistent organochlorine pesticide that poses threat to different life forms. Sphingobium indicum B90A that belong to sphingomonad is well-known for its ability to degrade HCH isomers (α-, β-, γ-, δ-), but effects of HCH isomers and adaptive mechanisms of strain B90A under HCH load remain obscure. To investigate th...
Mycobacterium tuberculosis is a known human pathogen that causes the airborne infectious disease tuberculosis (TB). Every year TB infects millions of people worldwide. The emergence of multi-drug resistant (MDR), extensively drug resistant (XDR) and totally drug resistant (TDR) M. tuberculosis strains against the first- and second-line anti-TB drug...
Silver carp is an invasive fish present in the Gobindsagar reservoir, India and has a profound impact on aquaculture. Understanding taxonomic diversity and functional attributes of gut microbiota will provide insights into the important role of bacteria in metabolism of silver carp that facilitated invasion of this exotic species. Microbial composi...
Adult specimens of Schistura montanus (McClelland) (syn. Nemacheilus kangrae Menon) were collected from Kamal river (78º05’ 36.4" E: 30º58’ 19.8" N; altitude 1375 MSL) of Uttarkashi district of Uttarakhand state, India. In the scale of S. montanus (McClelland), the focus region is neither similar to Indian major carps nor to minnows. The shape and...
The genus Sphingopyxis was first reported in the year 2001. Phylogenetically, Sphingopyxis is well delineated from other genera Sphingobium, Sphingomonas and Novosphingobium of sphingomonads group, family Sphingomonadaceae of Proteobacteria. To date (at the time of writing), the genus Sphingopyxis comprises of twenty validly published species avail...
Background:
Tor putitora, the largest freshwater fish of the Indian subcontinent, is an endangered species. Several factors have been attributed towards its continuous population decrease, but very little is known about the gut microbiome of this fish. Also, the fish gut microbiome serves as a reservoir of virulence factors and antibiotic resistan...
The COVID-19 pandemic continues to storm the world, with over 6.5 million cases worldwide. The severity of the disease varies with the territories and is mainly influenced by population density and age factor. In this study, we analyzed the transmission pattern of 95 SARS-CoV-2 genomes isolated from 11 different countries. Our study also revealed s...
A novel orange to pink coloured bacterial strain designated as CT19T was isolated from the gastrointestinal tract of mirror carp, Cyprinus carpio var. specularis (Lacepède, 1803) collected from the Gobind Sagar reservoir at village Lathiani, Una, Himachal Pradesh, India. Cells of the strain were found to be aerobic, Gram-stain-positive, non-motile...
The spirotrichean ciliate Stylonychia notophora has previously been recorded in India although the descriptions are lacking in detail. It has been suggested several times that the Indian population, S. notophora sensu Sapra and Dass, 1970 collected along the Delhi stretch of the River Yamuna, is identical to Tetmemena pustulata, but this has never...
The Coronavirus Disease-2019 (COVID-19) that started in Wuhan, China in December 2019 has spread worldwide emerging as a global pandemic. The severe respiratory pneumonia caused by the novel SARS-CoV-2 has so far claimed more than 60,000 lives and has impacted human lives worldwide. However, as the novel SARS-CoV-2 displays high transmission rates,...
Devosia are well known for their dominance in soil habitats contaminated with various toxins and are best characterized for their bioremediation potential. In this study, we compared the genomes of 27 strains of Devosia with aim to understand their metabolic abilities. The analysis revealed their adaptive gene repertoire which was bared from 52% un...
The discipline of genomics and metagenomics has been rapidly growing as an emerging field of research since the last decade. This development is largely due to the rapid advances in sequencing technologies that generate enormous amount of high throughput data at low costs. While there is huge information on genomics and metagenomics from different...
Members of genus Sphingopyxis are known to thrive in diverse environments. Genomes of 21 Sphingopyxis strains were selected. Phylogenetic analysis was performed using GGDC, AAI and core-SNP showed agreement at sub-species level. Based on our results, we propose that both S. baekryungensis DSM16222 and Sphingopyxis sp. LPB0140 strains should not be...
Metagenomics is the study of gene pool of an entire community in a particular niche. This provides valuable information about the functionality of host-microbe interaction in a biological ecosystem. Efficient metagenomic DNA extraction is a critical pre-requisite for a successful sequencing run in a metagenomic study. Although isolation of human st...
Different pattern of genetic diversity and population genetic structure among the species are reported due to their different ecological requirements, adaptability and the evolutionary histories. Understanding such patterns in a species and between the populations is important to develop the effective conservation plans. Very limited studies are av...
River Yamuna originates from Yamunotri in the Himalayas and is a major source for drinking water, hydropower generation and agricultural practices for a large stretch of land. Increased anthropogenic activities and discharge of domestic and industrial
wastes in this river has affected the water quality drastically. Out of the total distance (1370 K...
Here, we present the draft genome sequence of Deinococcus sp. strain S9, a red-pigmented and moderately thermophilic bacterium isolated from microbial mat deposits around the hot springs at Manikaran, Himachal Pradesh, India. The draft genome (3.34 Mb) contains 101 contigs with an average GC content of 66.4%.
A novel hypotrichous ciliate, Neogastrostyla aqua nov. gen., nov. spec. isolated from River Yamuna, Delhi, India, is described using morphological, morphometric and morphogenetic characters from live and stained cells supplemented with derivation of phylogenetic relationships using SSUrRNA gene. Neogastrostyla aqua nov. gen., nov. spec., is charact...
The present study was aimed to DNA extraction and PCR amplification of mitochondrial DNA of a varied size range using the non-invasive samples of fish. As many obstacles arise when obtaining an adequate amount of DNA from samples of endangered species, using non-invasive methods of sample collection and DNA extraction should be developed. To this e...
In recent years, investigations of microbial flora associated with fish gut have deepened our knowledge of the complex interactions occurring between microbes and host fish. The gut microbiome not only reinforces the digestive and immune systems in fish but is itself shaped by several host-associated factors. Unfortunately, in the past, majority of...
A novel oxytrichid ciliate was isolated from water samples collected at three locations
along the stretch of river Yamuna, Delhi, India. Morphological, morphometric and
morphogenetic studies were done using live and protargol stained cells and phylogenetic
studies were done using 18S rDNA gene and V4 region of 18S rDNA gene. The novel
oxytrichid is...
Abstract
Background and Objective: Heavy metals are one of the most common environmental pollutants and their presence in an aquatic
ecosystem has become a major global environmental problems. The pond in Bhagwanpur region is used for polyculture of major carps.
Rapid industrialization, sewage discharge, agricultural runoff and dumping of waste mat...
The current prokaryotic taxonomy classifies phenotypically and genotypically diverse microorganisms using a polyphasic approach. With advances in the next-generation sequencing technologies and computational tools for analysis of genomes, the traditional polyphasic method is complemented with genomic data to delineate and classify bacterial genera...
Thermophilic environments represent an interesting niche. Among thermophiles, the genus Thermus is among the most studied genera. In this study, we have sequenced the genome of Thermus parvatiensis strain RL, a thermophile isolated from Himalayan hot water springs (temperature >96°C) using PacBio RSII SMRT technique. The small genome (2.01 Mbp) com...
This study highlights the significant role of the genetic repertoire of a microorganism in the similarity between Novosphingobium strains. The results suggest that the phylogenetic relationships were mostly influenced by metabolic trait enrichment, which is possibly governed by the microenvironment of each microbe’s respective niche. Using core gen...
Phylogeography and evolutionary history of the freshwater species are poorly known. We document the phylogeography of widely distributed Puntius sophore using cytochrome oxidase subunit I (COI) gene of 650 bp. In the present study, we used 61 individual sequences from known geographic locations across India whereas data are lacking from other parts...
The great discrepancy in sequence divergence of congeneric (0.4-0.6%) and conspecific (3%) individuals makes it difficult to identify species using DNA. A 650 base pair fragment of the cytochrome c oxidase subunit I (COI) gene from the fish Pethia conchonius was analysed using 30 samples. All the samples were identified as P. conchonius and two oth...
Present study was designed and an attempt has been made to study the Scanning Electron Microscopy (SEM) and Energy Dispersive X-ray spectroscopy (EDAX) of fish of genus Puntius from Uttarakhand. Puntius conchonius and Puntius sophore (Spotted barbs) in the fast flowing water of Song River. The body of the fish in laterally compressed and is covered...
Aquatic ecosystem pollution by heavy metals is a worldwide concern. Heavy metals have the ability to bioaccumulate in aquatic organisms, particularly fish, which is a source of livelihood for humans. Between March 2012 and February 2014, we assessed heavy metal (Cu, Cr, Pb, Ni, Zn and Cd) contamination in two food fish species (Labeo rohita and Hyp...
The study was undertaken to assess the phytoplankton diversity in relation to abiotic factors of Nainital lake of Kumaon Himalayas of Uttarakhand State, India. The samples were collected from the three selected study sites for the period from May, 2007 to April, 2009. A total of 25 genera of phytoplankton were reported belonging to 3 groups viz., b...
Genetic based study provide emphasis on the population study of geographically isolated population, gene flow among them and evolutionary history of the species. In the present study, we aimed to detect the genetic variations in species of genus Schistura from Uttarakhand. Very little is known for the pattern of distribution and genetic diversity o...
The length-weight relationship (LWR) and condition factor (K) for two commercially important carps (Labeo rohita and Hypophthalmichthys molitrix) was carried out in two fish ponds in and around Roorkee ,Haridwar (Uttrakhand).The samples were collected in four different seasons (spring, summer, autumn and winter) from March 2012 to February 2013. In...
During the present investigation a total of six sampling population of Schistura montanus from the Garhwal and Kumaun region with total 24 morphometric parameters were analyzed. A total of 39 samples were collected from the Garhwal and Kumaun regions of Uttarakhand state. As the very little information on this species available based on the morphol...
Present investigation was carried out to assess the seasonal variation of benthic macro-invertebrates from the Tons river, a tributary of Yamuna River in Garhwal Himalaya, Uttrakhand during December, 2007 to November, 2009. The seasonal benthic diversity was correlated with various physic-chemical parameters which documented that the macrobenthic d...
In the present study samples were collected from the three different locations of Tons river of Uttarkhand State from December, 2007 to November, 2009 on the monthly basis for the study of zooplankton diversity. During the present investigation, a total of 23 genera of zooplankton belonging to 7 major groups viz. Ciliophore, Cladocera, Copepod, Por...
Over the last century, riverine ecosystems have suffered from intense human intervention resulting in habitat loss and degradation and as a consequence, many fish species have become highly endangered, particular in rivers where heavy demand is placed on freshwaters. In present study three study sites were selected along the stretch of river Tons....
Four sampling stations viz. Site-I (Control), Site-II (Discharge point), Site-III (500 m from discharge point) and Site-IV
(1000 m from discharge point) were selected for faunal analysis to study effect of pulp and paper mill effluent on the
diversity of zooplankton in the Ganga River water at Bijnor (UP) India. 19 genera of zooplankton belonging...
This investigation was carried out to examine the diversity of phytoplankton in Bhimtal lake of Uttarakhand state, India. Various water parameters were correlated with phytoplankton diversity. Sampling was carried out during May 2007 to April 2009. A total 19 genera of phytoplankton belonging to three groups viz. bacillariophyceae (8 genera), chlor...
The present investigation has been carried out from March, 2005 to Feb., 2007 in order to determine the seasonal variation of phytoplankton from Ganga river and its tributaries. Samples were collected from four different stations. Three phytoplankton samples were collected from stream and one sample from Ganga river. Plankton samples were taken usi...
The present investigation has been carried out from March, 2005 to Feb., 2007 in order to determine the seasonal variation of phytoplankton from Ganga river and its tributaries. Samples were collected from four different stations. Three phytoplankton samples were collected from stream and one sample from Ganga river. Plankton samples were taken usi...
During the present investigation, a total of 9 species belonged to 6 genera, 2 families and 2 orders were reported from the Nainital Lake. Out of 6 genera, genus Puntius (48.46%) was the most dominant genera followed by Schizothorax richardosonii (12.90%), Gambusia (8.87%), Labeo rohita (4.83%), Cyprinus (4.03%) and Catla (2.41%). From Bhimtal Lake...
A study on morphometric characters of snow trout fish Schizothorax richardsonii (Gray) was conducted on the samples collected from Yamuna river of the Uttarakashi district of Uttarakhand State. The morphometric measurements such as total length, standard length, predorsal distance, preventral distance, preanal distance, maximum body depth, minimum...
Fish diversity in different habitats and their preference for a particular habitat was studied in a freshwater stream Hinval in Western Himalayas of Garhwal region. A total of 7 fish species belonging to 2 orders were recorded. The maximum fish diversity and dominance was reported in the cyprinids. Two species of order Cypriniformes, Tor putitora (...
